Its good that you got it out of that ceramic pot. The good news is that you do have some good roots in there. The roots that are plump and greenish are healthy, happy roots. The yellow, mushy or dried roots are obviously dead. The yellow leaves are a direct result of being overwatered.
The petals look like mechanical damage - overwatering results in wilted flowers, not bruised and holey flowers.
Your Phalaenopsis has enough roots to do well and will grow more with proper care. Phals like to be dry so if you stick your finger in the bark and feel any moisture, don't water. When you do water, fill the ceramic pot with water and let the bark soak for 5 minutes then dump the water out.